LAP3

leucine aminopeptidase 3, the group of Aminopeptidases

Basic information

Region (hg38): 4:17577198-17607972

Previous symbols: [ "PEPS" ]

Links

ENSG00000002549 ∙ NCBI:51056 ∙ OMIM:170250 ∙ HGNC:18449 ∙ Uniprot:P28838 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	1		23
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	25	1	0

Variants in LAP3

This is a list of pathogenic ClinVar variants found in the LAP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-17577475-C-A		not specified	Uncertain significance (Jan 31, 2024)
4-17577481-C-T		not specified	Uncertain significance (Jun 07, 2024)
4-17577508-C-G		not specified	Uncertain significance (Oct 26, 2022)
4-17577520-G-T		not specified	Uncertain significance (Jun 27, 2023)
4-17577526-C-T		not specified	Uncertain significance (Jul 20, 2021)
4-17577560-T-G		not specified	Uncertain significance (Nov 07, 2022)
4-17579840-T-C		not specified	Uncertain significance (Oct 27, 2022)
4-17582352-A-C		not specified	Uncertain significance (Oct 06, 2022)
4-17583624-C-T		not specified	Uncertain significance (Mar 31, 2022)
4-17583639-G-A		not specified	Uncertain significance (Aug 26, 2022)
4-17585075-T-A		not specified	Uncertain significance (Oct 03, 2022)
4-17585081-G-A		not specified	Uncertain significance (Oct 27, 2021)
4-17585103-A-G		not specified	Likely benign (Sep 12, 2023)
4-17585111-A-G		not specified	Uncertain significance (May 13, 2024)
4-17585115-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-17588844-G-A		not specified	Uncertain significance (Oct 20, 2021)
4-17588850-G-A		not specified	Uncertain significance (Jun 13, 2023)
4-17595532-T-C		not specified	Uncertain significance (Oct 20, 2023)
4-17597078-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-17598529-A-C		not specified	Uncertain significance (Dec 27, 2023)
4-17598538-T-A		not specified	Uncertain significance (Jan 03, 2024)
4-17604588-G-A		not specified	Uncertain significance (Sep 27, 2021)
4-17604595-G-A		not specified	Uncertain significance (May 30, 2024)
4-17604651-G-C		not specified	Uncertain significance (Sep 22, 2022)
4-17604652-G-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAP3	protein_coding	protein_coding	ENST00000226299	13	30781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-7	0.957	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	246	299	0.822	0.0000161	3386
Missense in Polyphen		89	125.69	0.7081		1363
Synonymous	-0.284	118	114	1.03	0.00000716	1014
Loss of Function	1.96	15	25.7	0.583	0.00000116	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000365
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00310	0.00310
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.00310	0.00310
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);Glutathione metabolism - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.643

Intolerance Scores

• loftool: 0.728
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.65

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.368
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lap3

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;nucleoplasm;trans-Golgi network;cytosol;focal adhesion;midbody;extracellular exosome
• Molecular function: aminopeptidase activity;metalloexopeptidase activity;manganese ion binding